Nature is considered an indispensable source of natural products and natural products-derived drug leads. Over the last decade, the use of natural products-based medicine (herbal medicine or phytomedicine) has increased tremendously worldwide especially with the exceeding prevalence of metabolic disorders. Metabolic disorders are the major worldwide epidemic associated with obesity, diabetes mellitus, cardiovascular diseases associated with hyperlipidemia, and many other endocrine and nutrition-related issues. Since metabolic disorders are multi-factorial in their pathophysiology, they can be targeted by natural products that have synergy between diverse metabolites. Therefore, it is important to find the proper formulas not only for the treatment but also for reduction of associated risks and for prophylaxis and prevention of long-term complications. At the present work, a brief outline of the pathophysiology of metabolic disorders is provided. Additionally, natural product based drug therapies that are currently applied in clinical trials attributed to metabolic related diseases are critically discussed.